A dedicated Starfleet officer, Archer's desire for his own command landed him in the center seat of an advanced starship from another time and place. However, his quest for power and glory, and his ultimate desire to take over the Terran Empire, eventually resulted in his downfall, but Archer's actions may very well have ushered in a new era for the Empire.

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Archer was actually in line to command the ISS Enterprise himself, but CaptainMaximilian Forrest assumed command instead. Archer insisted that this change of command was the result of an unspecified number of admirals conspiring against him.

Prior to serving aboard Enterprise, Archer was romantically involved with Hoshi Sato. When Forrest was given captaincy of Enterprise, however, Sato, seeing an opportunity to advance her career, left Archer to become the captain's woman. Although Archer claimed to understand that Sato leaving him was strictly a career move, he was nonetheless hurt and resentful.

Despite taking away Archer's command and his lover, Forrest selected Archer as his first officer. He later claimed that he trusted Archer because he felt Archer never sought power and glory, and that he had no ambition. But Archer did indeed harbor ambition for his own command, and it was only a matter of time before those ambitions surfaced.

In 2155, after finding scans of an Earth ship from the future – later discovered to be the USS Defiant – Archer tried to convince Forrest to go after that ship. When Forrest refused, Archer mutinied to find the Defiant and use its technology to aid the Terran Empire. When Archer assumed command of Enterprise, he made T'Pol his first officer, and ordered her and chief engineer Commander Charles Tucker III to install a Sulibancloaking device on the ship and set a heading into Tholian space to find the Defiant. After T'Pol helped Forrest regain his command, Archer was thrown in the agony booth for a record ten hours. When Forrest was forced to continue the mission at the behest of Starfleet, Archer briefed the senior staff on the origin of that ship.

After arriving at the vessel's coordinates, Archer commanded an away team to the Defiant, and Forrest ordered T'Pol to make sure that Archer didn't come back alive. While on the Defiant, Enterprise was destroyed, and Archer was able to take control of the Defiant and head toward Terran space.

While aboard the Defiant, Archer learned about his counterpart in the mirror universe, CaptainJonathan Archer. At first, he protested that his counterpart was not a great man but weak and foolish for his efforts in helping to form the United Federation of Planets (which he dismissed as a "Federation of Fools"), noting that great men should conquer other species, not work together with them. Secretly, however, Archer resented his counterpart and was insanely jealous of his success, particularly when he learned that the "other" Archer had a long, respected career as a starship captain, diplomat, and statesman, had two planets named for him, and was noted as the "greatest explorer of the 22nd century." His preoccupation with his counterpart's success eventually drove him to have hallucinations of the "other" Archer, who mercilessly taunted him about his own inadequacies.

Archer became determined to gain the same respect and hero status accorded to his normal universe counterpart. When it was determined that Slar, the Gorn foreman that was employed by the Tholians, was responsible for stealing key engine components and indiscriminately murdering several engineers, Archer rejected T'Pol's advice to negotiate with him. Seeing an opportunity to earn the respect of his crew, he, encouraged by his illusory counterpart, personally led a team of MACOs to the lower decks of the Defiant to seek out and kill Slar. The ill-advised operation resulted in a bloody pyrrhic victory. During the pursuit, MajorMalcolm Reed was seriously injured, and other MACOs were killed. Archer himself nearly died at Slar's hands before ultimately defeating and killing the Gorn.

When the Defiant eventually made it to the battle between both Starfleet and rebel forces, the ISS Avenger, under the command of Admiral Black, was the only surviving Starfleet vessel. Archer destroyed all but one of the rebel ships, as he wanted the rebels to learn what had transpired. Black was grateful to Archer for both his intervention in the battle and for obtaining the Defiant, and assured Archer he would be promoted at the earliest opportunity. When Archer asked for an immediate battlefield promotion and command of the Defiant on a permanent basis, Black refused, stating he wanted to take the ship back to Earth as a trophy and have it reverse-engineered to learn about its technology. Archer, fed up with the continuing losses suffered by the Empire, its corrupt leadership, the setbacks his own career was suffering, and the realization that Black would likely take all the credit for his own achievements (all the while being taunted by his illusory counterpart), finally reached his breaking point. In a bold move, he murdered Black and took the Defiant for himself.

In an address before the crews of the Avenger and the Defiant, Archer unveiled his most ambitious plan yet: seizing control of the Terran Empire. He argued that the problem with the Empire was its leadership, and publicly announced that he was seeking to make himself emperor and then stop the rebellion.

In the process of approaching Earth, Archer became more anti-alien in his views, believing they were holding Humanity back. In his paranoia, he ordered all alien crewmembers (with the exception of Dr.Phlox, who he believed would not be a threat as his species were known pacifists) on the Defiant transferred onto the Avenger. Archer later destroyed the Avenger as its alien crew, led by Soval, attempted to stop him.

As the Defiant made its way to Earth, Archer was apparently poisoned by Hoshi Sato (with assistance from SergeantTravis Mayweather), who decided to take the crown for herself.